I need help clarifying the differences in Advanced Sholl Analysis output depending on which arbor value I use.
I'm using a binarized (background=0) skeleton image and when I place the starting point on the path (as described on
http://fiji.sc/wiki/index.php/Simple_Neurite_Tracer:_Sholl_analysis) I get the following output:
java.lang.ArrayIndexOutOfBoundsException: 255
at Advanced_Sholl_Analysis.run(Advanced_Sholl_Analysis.java:162)
at ij.IJ.runUserPlugIn(IJ.java:184)
at ij.IJ.runPlugIn(IJ.java:151)
at ij.Executer.runCommand(Executer.java:127)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)
If I place the starting point off the path, I have the option of selecting the arbor value (0, 255), but I get two different outputs depending on which value I choose. The arbor value of the image on the left is 0 and the value of the image on the right is 255.
1. Am I correct in assuming that the difference is where the center of the rings is generated (the closest point with the same/different value as the defined arbor value)?
2. Why are the Intersections Masks different?
3. Does it matter which value I use and why?
Thanks in advance for your help!